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Work is fun
Sep. 8th, 2006 08:47 pmI didn't have much fun doing academic research, but building the tools that researchers can use does appeal to me. Yesterday, I solved the structure of a protein.
That is, I took some diffraction images collected as a calibration exercise on Tuesday at the ESRF synchrotron at Grenoble, downloaded the PDB entry for trypsin, and got one of our company's products to convert the images to merged intensities and another to convert the merged intensities to a protein structure. It required the invocation of three programs with four command-line options apiece, an hour and a half of processing on a computer which cost £800 last year, and a total of nearly two minutes of thought, spent figuring out which the positive X direction on the detector was.
Today, I did Porcine Olfactory Protein; this is a small protein found in abundance in pig snot, which binds promiscuously to a vast number of odiferous molecules. I took data for one of its bound forms (PDB 1E00), removed the ligand, collected someone else's intensity measurements for a different bound form (PDB 1DZJ), invoked REFINE, waited an hour, and got a pretty purple and green 3D diagram in which you could see what the new ligand (a peculiar pungent selenium- and nitrogen-containing heterocycle) was doing.
Max Perutz and John Kendrew took thirteen years of false starts plus nine years of concerted effort to compute a protein structure in 1960, the first time it was done, and won a Nobel Prize thereby. It now makes for a slightly upmarket GCSE biology exercise, for which the tedious part for the teacher would be getting licenses to the necessary software. I do like the twenty-first century.
That is, I took some diffraction images collected as a calibration exercise on Tuesday at the ESRF synchrotron at Grenoble, downloaded the PDB entry for trypsin, and got one of our company's products to convert the images to merged intensities and another to convert the merged intensities to a protein structure. It required the invocation of three programs with four command-line options apiece, an hour and a half of processing on a computer which cost £800 last year, and a total of nearly two minutes of thought, spent figuring out which the positive X direction on the detector was.
Today, I did Porcine Olfactory Protein; this is a small protein found in abundance in pig snot, which binds promiscuously to a vast number of odiferous molecules. I took data for one of its bound forms (PDB 1E00), removed the ligand, collected someone else's intensity measurements for a different bound form (PDB 1DZJ), invoked REFINE, waited an hour, and got a pretty purple and green 3D diagram in which you could see what the new ligand (a peculiar pungent selenium- and nitrogen-containing heterocycle) was doing.
Max Perutz and John Kendrew took thirteen years of false starts plus nine years of concerted effort to compute a protein structure in 1960, the first time it was done, and won a Nobel Prize thereby. It now makes for a slightly upmarket GCSE biology exercise, for which the tedious part for the teacher would be getting licenses to the necessary software. I do like the twenty-first century.
